[English] 日本語
![](img/lk-miru.gif)
- EMDB-29700: Cryo-EM imaging scaffold subunits A and B used to display KRAS G1... -
+
Open data
-
Basic information
Entry | ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM imaging scaffold subunits A and B used to display KRAS G12C complex with GDP | |||||||||
![]() | scaffold subunits A and B used to display KRAS G12C complex with GDP![]() | |||||||||
![]() |
| |||||||||
![]() | CryoEM imaging scaffold / ![]() ![]() ![]() | |||||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() | |||||||||
Biological species | synthetic construct (others) / ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Castells-Graells R / Sawaya MR / Yeates TO | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Cryo-EM structure determination of small therapeutic protein targets at 3 Å-resolution using a rigid imaging scaffold. Authors: Roger Castells-Graells / Kyle Meador / Mark A Arbing / Michael R Sawaya / Morgan Gee / Duilio Cascio / Emma Gleave / Judit É Debreczeni / Jason Breed / Karoline Leopold / Ankoor Patel / ...Authors: Roger Castells-Graells / Kyle Meador / Mark A Arbing / Michael R Sawaya / Morgan Gee / Duilio Cascio / Emma Gleave / Judit É Debreczeni / Jason Breed / Karoline Leopold / Ankoor Patel / Dushyant Jahagirdar / Bronwyn Lyons / Sriram Subramaniam / Chris Phillips / Todd O Yeates / ![]() ![]() ![]() Abstract: Cryoelectron microscopy (Cryo-EM) has enabled structural determination of proteins larger than about 50 kDa, including many intractable by any other method, but it has largely failed for smaller ...Cryoelectron microscopy (Cryo-EM) has enabled structural determination of proteins larger than about 50 kDa, including many intractable by any other method, but it has largely failed for smaller proteins. Here, we obtain structures of small proteins by binding them to a rigid molecular scaffold based on a designed protein cage, revealing atomic details at resolutions reaching 2.9 Å. We apply this system to the key cancer signaling protein KRAS (19 kDa in size), obtaining four structures of oncogenic mutational variants by cryo-EM. Importantly, a structure for the key G12C mutant bound to an inhibitor drug (AMG510) reveals significant conformational differences compared to prior data in the crystalline state. The findings highlight the promise of cryo-EM scaffolds for advancing the design of drug molecules against small therapeutic protein targets in cancer and other human diseases. | |||||||||
History |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 86.1 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 16.7 KB 16.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.2 KB | Display | ![]() |
Images | ![]() | 62.3 KB | ||
Others | ![]() ![]() | 84.7 MB 84.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8g3kMC ![]() 8g42C ![]() 8g47C ![]() 8g4eC ![]() 8g4fC ![]() 8g4hC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | scaffold subunits A and B used to display KRAS G12C complex with GDP | ||||||||||||||||||||
Voxel size | X=Y=Z: 1 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: Half Map 1
File | emd_29700_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half Map 1 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half Map 2
File | emd_29700_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half Map 2 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : Cryo-EM imaging scaffold displaying KRAS G12C
Entire | Name: Cryo-EM imaging scaffold displaying KRAS G12C |
---|---|
Components |
|
-Supramolecule #1: Cryo-EM imaging scaffold displaying KRAS G12C
Supramolecule | Name: Cryo-EM imaging scaffold displaying KRAS G12C / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: synthetic construct (others) |
-Macromolecule #1: Cob_adeno_trans domain-containing protein
Macromolecule | Name: Cob_adeno_trans domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 20.173395 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MRITTKVGDK GSTRLFGGEE VWKDDPIIEA NGTLDELTSF IGEAKHYVDE EMKGILEEIQ NDIYKIMGEI GSKGKIEGIS EERIKWLAG LIERYSEMVN KLSFVLPGGT LESAKLDVCR TIARRAERKV ATVLREFGIG TLAAIYLALL SRLLFLLARV I EIEKNKLK EVRSHHHHHH UniProtKB: Cobalamin adenosyltransferase-like domain-containing protein |
-Macromolecule #2: Cryo-EM imaging scaffold subunit B with DARPin - RCG-33
Macromolecule | Name: Cryo-EM imaging scaffold subunit B with DARPin - RCG-33 type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 35.452441 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MFTRRGDQGE TDLANRARVG KDSPVVEVQG TIDELNSFIG YALVLSRWDD IRNDLFRIQN DLFVLGEDVS TGGKGRTVTM DMIIYLIKR SVEMKAEIGK IELFVVPGGS VESASLHMAR AVSRRLERRI KAASELTEIN ANVLLYANML SNILFMHALI S NKRKEELD ...String: MFTRRGDQGE TDLANRARVG KDSPVVEVQG TIDELNSFIG YALVLSRWDD IRNDLFRIQN DLFVLGEDVS TGGKGRTVTM DMIIYLIKR SVEMKAEIGK IELFVVPGGS VESASLHMAR AVSRRLERRI KAASELTEIN ANVLLYANML SNILFMHALI S NKRKEELD KKLLEAARAG QDDEVAALLA KGADVNAHDT FGFTPLHLAA LYGHLEIVEV LLKRGADINA DDSYGRTPLH LA AMRGHLE IVELLLRWGA DVNAADEEGR TPLHLAAKRG HLEIVEVLLK NGADVNAQDK FGKTAFDISI DNGNEDLAEI LQK L |
-Experimental details
-Structure determination
Method | ![]() |
---|---|
![]() | ![]() |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 8 |
---|---|
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
-
Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
---|---|
Output model | ![]() PDB-8g3k: |